[Chimera-users] Offsetting residue numbering

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 22 10:55:10 PDT 2011

Hi Sumitro,
I would renumber the residues in the input file before opening it in Chimera.  Of course, manual editing is too tedious.  One of these web servers for PDB editing may be the most convenient:


Uh-oh,  the second one is unreachable currently.  I'm hoping it's temporary... but at least the first one is still there.

I believe they both make you choose or upload the file before you can see the options, but can  do several things, including changing chain ID and renumbering the residues.
I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 22, 2011, at 6:33 AM, Sumitro Harjanto wrote:

> Hi Elaine,
> Is there a way to introduce a systematic offset to the residue numbering in a model?
> The numbering in my model is different from the convention. Eg. the methionine that's supposedly in position 5 is labeled as MET 4, alanine in position 6 as ALA 5, and so on. I can't do it manually cos there are many residues. Is there an easy way to resolve this other than using a script to automatically assign the labels? It'll be good if i can resolve this from the root , such that my atom specification is also consistent with the naming convention I use. :)
> Cheers,
> Sumitro

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